Evidence map›Paper›PMID 33900378›Full record

ArticleDatabase : the journal of biological databases and curation2021

Tripal MegaSearch: a tool for interactive and customizable query and download of big data.

Sook Jung, Chun-Huai Cheng, Katheryn Buble, Taein Lee, Jodi Humann, Jing Yu, James Crabb, Heidi Hough, Dorrie Main

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Building resource-efficient community databases using open-source software.Database : the journal of biological databases and curation · 2025
    Article
  5. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota).Database : the journal of biological databases and curation · 2022
    Article
  6. Article
  7. Article
  8. The Breeding Information Management System (BIMS): an online resource for crop breeding.Database : the journal of biological databases and curation · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Sook JungDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Chun-Huai ChengDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Katheryn BubleDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Taein LeeDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Jodi HumannDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Jing YuDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
James CrabbDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Heidi HoughDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.
Dorrie MainDepartment of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tripal MegaSearch is a Tripal module for querying and downloading biological data stored in Chado. This module allows site users to select data types, restrict the dataset by applying various filters and then customizing fields to view and download through a single interface. Set by site administrators, example data types include gene, germplasm, marker, map, QTL, genotype, phenotype and expression data. When querying for genes, users can restrict the gene dataset using various filters such as name, chromosome position and functional annotation. They can then customize fields to download, such as name, organism, type, chromosome position, various functional annotations such as BLAST, KEGG, InterPro and GO term. FASTA files can also be downloaded for the sequence data. Site administrators can choose from two different data sources to serve data: Tripal MegaSearch materialized views or Chado tables. If neither data source is desired, administrators may also create their own materialized views and serve them through the flexible dynamic Tripal MegaSearch query form. Tripal MegaSearch is currently implemented in several databases including the Genome Database for Rosaceae www.rosaceae.org and TreeGenes www.https://treegenesdb.org/.

Indexed as

Databases, GeneticGenomicsBig DataGenotypeInformation Storage and RetrievalInternetSoftwareUser-Computer Interface

Identifiers

PMID33900378
PMCPMC8074878

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.